[{"author":[{"last_name":"Marveggio","first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","full_name":"Marveggio, Alice"}],"related_material":{"record":[{"id":"11842","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"14597"}]},"date_created":"2023-11-21T11:41:05Z","date_updated":"2024-03-22T13:21:28Z","year":"2023","acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-03-20T12:28:32Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","doi":"10.15479/at:ista:14587","supervisor":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"month":"11","publication_identifier":{"issn":["2663 - 337X"]},"file":[{"access_level":"open_access","file_name":"thesis_Marveggio.pdf","content_type":"application/pdf","file_size":2881100,"creator":"amarvegg","relation":"main_file","file_id":"14626","checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","success":1,"date_updated":"2023-11-29T09:09:31Z","date_created":"2023-11-29T09:09:31Z"},{"file_size":10189696,"content_type":"application/zip","creator":"amarvegg","file_name":"Thesis_Marveggio.zip","access_level":"closed","date_created":"2023-11-29T09:10:19Z","date_updated":"2024-03-20T12:28:32Z","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","relation":"source_file","file_id":"14627"}],"oa_version":"Published Version","_id":"14587","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","ddc":["515"],"abstract":[{"lang":"eng","text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2023-11-21T00:00:00Z","citation":{"ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria.","ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","apa":"Marveggio, A. (2023). Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14587","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587","chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14587.","mla":"Marveggio, Alice. Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14587.","short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023."},"page":"228","day":"21","article_processing_charge":"No","has_accepted_license":"1"},{"file_date_updated":"2024-02-08T23:30:04Z","author":[{"full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","first_name":"Bettina"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8586"}]},"date_created":"2023-02-02T14:50:20Z","date_updated":"2024-03-25T23:30:05Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"month":"02","publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:12491","supervisor":[{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"abstract":[{"text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_name":"PhDThesis_BettinaZens_2023_final.pdf","access_level":"open_access","creator":"bzens","file_size":23082464,"content_type":"application/pdf","embargo":"2024-02-07","file_id":"12527","relation":"main_file","date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:07:38Z","checksum":"069d87f025e0799bf9e3c375664264f2"},{"access_level":"closed","file_name":"PhDThesis_BettinaZens_2023_final.docx","embargo_to":"open_access","creator":"bzens","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":106169509,"file_id":"12528","relation":"source_file","checksum":"8c66ed203495d6e078ed1002a866520c","date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:09:05Z"}],"oa_version":"Published Version","_id":"12491","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","status":"public","ddc":["570"],"day":"02","article_processing_charge":"No","has_accepted_license":"1","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"date_published":"2023-02-02T00:00:00Z","citation":{"chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491"},"page":"187"},{"publication_identifier":{"issn":["2791-4585"]},"month":"08","doi":"10.15479/at:ista:14226","language":[{"iso":"eng"}],"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}],"degree_awarded":"MS","oa":1,"file_date_updated":"2024-02-26T23:30:03Z","author":[{"full_name":"Stephenson, Elizabeth R","last_name":"Stephenson","first_name":"Elizabeth R","orcid":"0000-0002-6862-208X","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-26T23:30:04Z","date_created":"2023-08-24T13:01:18Z","year":"2023","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"24","date_published":"2023-08-24T00:00:00Z","citation":{"chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226.","mla":"Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","apa":"Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226"},"page":"43","abstract":[{"lang":"eng","text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes."}],"type":"dissertation","alternative_title":["ISTA Master's Thesis"],"oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":15501411,"content_type":"application/x-zip-compressed","file_name":"documents-export-2023-08-24.zip","embargo_to":"open_access","access_level":"closed","date_created":"2023-08-24T13:02:49Z","date_updated":"2024-02-26T23:30:03Z","checksum":"453caf851d75c3478c10ed09bd242a91","file_id":"14227","relation":"source_file"},{"creator":"cchlebak","file_size":6854783,"content_type":"application/pdf","file_name":"thesis_pdf_a.pdf","access_level":"open_access","date_updated":"2024-02-26T23:30:03Z","date_created":"2023-08-24T13:03:42Z","checksum":"7349d29963d6695e555e171748648d9a","file_id":"14228","embargo":"2024-02-25","relation":"main_file"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"14226","ddc":["500"],"title":"Generalizing medial axes with homology switches","status":"public"},{"date_created":"2023-01-31T15:10:53Z","date_updated":"2023-08-31T12:26:58Z","author":[{"last_name":"Michalska","first_name":"Julia M","orcid":"0000-0003-3862-1235","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11943"},{"id":"11950","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"publisher":"Institute of Science and Technology Austria","year":"2023","file_date_updated":"2023-07-27T22:30:54Z","ec_funded":1,"supervisor":[{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12470","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"01","publication_identifier":{"isbn":[" 978-3-99078-026-8"],"issn":["2663-337X"]},"file":[{"file_id":"12471","embargo":"2023-07-09","relation":"main_file","date_updated":"2023-07-27T22:30:54Z","date_created":"2023-01-31T15:11:42Z","checksum":"1a2306e5f59f52df598e7ecfadf921ac","file_name":"20230109_PhD_thesis_JM_final.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":41771714},{"checksum":"0bebbdee0773443959e1f6ab8caf281f","date_updated":"2023-07-10T22:30:04Z","date_created":"2023-01-31T15:11:51Z","relation":"source_file","file_id":"12472","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":66983464,"creator":"cchlebak","access_level":"closed","embargo_to":"open_access","file_name":"20230109_PhD_thesis_JM_final.docx"}],"oa_version":"Published Version","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","ddc":["610"],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12470","abstract":[{"lang":"eng","text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2023-01-09T00:00:00Z","page":"201","citation":{"chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470.","mla":"Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470.","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470"},"day":"09","has_accepted_license":"1","article_processing_charge":"No"},{"has_accepted_license":"1","article_processing_charge":"No","day":"08","citation":{"ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:10.15479/at:ista:12531","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","apa":"Kirillova, K. (2023). Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","mla":"Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531."},"page":"46","date_published":"2023-02-08T00:00:00Z","type":"dissertation","alternative_title":["ISTA Master's Thesis"],"abstract":[{"lang":"eng","text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics."}],"_id":"12531","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Panoramic functional gradients across the mouse retina","ddc":["570"],"status":"public","file":[{"access_level":"open_access","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","file_size":8369317,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"12532","embargo":"2024-02-08","checksum":"57d8da3a6c749eb1556b7435fe266a5f","date_created":"2023-02-09T08:03:32Z","date_updated":"2024-02-09T23:30:03Z"},{"relation":"source_file","file_id":"12535","date_created":"2023-02-10T09:32:06Z","date_updated":"2024-02-09T23:30:03Z","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","embargo_to":"open_access","file_name":"Thesis Kseniia - 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Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. ","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Master's Thesis"],"date_published":"2023-04-05T00:00:00Z","citation":{"ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","apa":"Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","mla":"Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800.","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800."},"page":"21","has_accepted_license":"1","article_processing_charge":"No","day":"05"},{"date_published":"2023-11-10T00:00:00Z","citation":{"short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria."},"page":"180","day":"10","article_processing_charge":"No","has_accepted_license":"1","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"file":[{"file_name":"Thesis_Gnyliukh_final_08_11_23.docx","access_level":"closed","file_size":20824903,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"ngnyliuk","relation":"source_file","file_id":"14567","date_updated":"2023-11-20T09:18:51Z","date_created":"2023-11-20T09:18:51Z","checksum":"3d5e680bfc61f98e308c434f45cc9bd6"},{"date_updated":"2023-11-23T13:10:55Z","date_created":"2023-11-20T09:23:11Z","checksum":"bfc96d47fc4e7e857dd71656097214a4","file_id":"14568","embargo":"2024-11-23","relation":"main_file","creator":"ngnyliuk","file_size":24871844,"content_type":"application/pdf","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","embargo_to":"open_access","access_level":"closed"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"14510","ddc":["570"],"status":"public","title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:14510","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"month":"11","publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"author":[{"full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"}],"related_material":{"record":[{"id":"14591","relation":"part_of_dissertation","status":"public"},{"id":"9887","relation":"part_of_dissertation","status":"public"},{"id":"8139","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2024-03-28T23:30:46Z","date_created":"2023-11-10T09:10:06Z","year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-11-23T13:10:55Z","ec_funded":1},{"date_published":"2023-05-05T00:00:00Z","page":"180","citation":{"mla":"Hafner, Christian. Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12897.","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12897.","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","apa":"Hafner, C. (2023). Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12897","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023."},"day":"05","has_accepted_license":"1","article_processing_charge":"No","file":[{"file_size":50714445,"content_type":"application/pdf","creator":"chafner","file_name":"thesis-hafner-2023may11-a2b.pdf","access_level":"open_access","date_created":"2023-05-11T10:43:20Z","date_updated":"2023-12-08T23:30:04Z","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","relation":"main_file","file_id":"12942","embargo":"2023-12-07"},{"date_updated":"2023-12-08T23:30:04Z","date_created":"2023-05-11T10:43:44Z","checksum":"a6b51334be2b81672357b1549afab40c","relation":"source_file","file_id":"12943","content_type":"application/pdf","file_size":265319,"creator":"chafner","embargo_to":"open_access","file_name":"thesis-release-form.pdf","access_level":"closed"}],"oa_version":"Published Version","ddc":["516","004","518","531"],"status":"public","title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","_id":"12897","user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","acknowledged_ssus":[{"_id":"M-Shop"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12897","project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"oa":1,"month":"05","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-031-2"]},"date_updated":"2024-01-29T10:47:51Z","date_created":"2023-05-05T10:40:14Z","author":[{"last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9817"},{"relation":"part_of_dissertation","status":"public","id":"7117"},{"relation":"dissertation_contains","status":"public","id":"13188"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","year":"2023","file_date_updated":"2023-12-08T23:30:04Z","ec_funded":1},{"date_published":"2022-09-08T00:00:00Z","page":"208","citation":{"ieee":"A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022.","apa":"Shute, A. L. (2022). Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12072","ista":"Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria.","ama":"Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:10.15479/at:ista:12072","chicago":"Shute, Alec L. “Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12072.","short":"A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.","mla":"Shute, Alec L. Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12072."},"day":"08","has_accepted_license":"1","article_processing_charge":"No","oa_version":"Published Version","file":[{"file_name":"Thesis_final_draft.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1907386,"creator":"ashute","relation":"main_file","file_id":"12073","date_updated":"2022-09-08T21:50:34Z","date_created":"2022-09-08T21:50:34Z","checksum":"bf073344320e05d92c224786cec2e92d","success":1},{"content_type":"application/octet-stream","file_size":495393,"creator":"ashute","access_level":"closed","file_name":"athesis.tex","checksum":"b054ac6baa09f70e8235403a4abbed80","date_updated":"2022-09-12T11:24:21Z","date_created":"2022-09-08T21:50:42Z","relation":"source_file","file_id":"12074"},{"relation":"source_file","file_id":"12078","checksum":"0a31e905f1cff5eb8110978cc90e1e79","date_created":"2022-09-09T12:05:00Z","date_updated":"2022-09-12T11:24:21Z","access_level":"closed","file_name":"qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip","file_size":944534,"content_type":"application/x-zip-compressed","creator":"ashute"}],"status":"public","title":"Existence and density problems in Diophantine geometry: From norm forms to Campana points","ddc":["512"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12072","abstract":[{"lang":"eng","text":"In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm\r\nform associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations.\r\nIn the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or\r\nintegral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points.\r\nMore precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in\r\nthe power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","supervisor":[{"first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12072","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"month":"09","publication_identifier":{"isbn":["978-3-99078-023-7"],"issn":["2663-337X"]},"date_created":"2022-09-08T21:53:03Z","date_updated":"2023-02-21T16:37:35Z","author":[{"full_name":"Shute, Alec L","first_name":"Alec L","last_name":"Shute","id":"440EB050-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1812-2810"}],"related_material":{"record":[{"id":"12076","status":"public","relation":"part_of_dissertation"},{"id":"12077","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"TiBr"}],"acknowledgement":"I acknowledge the received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie Grant Agreement No. 665385.","year":"2022","file_date_updated":"2022-09-12T11:24:21Z","ec_funded":1},{"page":"170","citation":{"mla":"Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes. Institute of Science and Technology, 2022, doi:10.15479/at:ista:11777.","short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022.","chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology, 2022. https://doi.org/10.15479/at:ista:11777.","ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:10.15479/at:ista:11777","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology.","apa":"Wild, P. (2022). High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology. https://doi.org/10.15479/at:ista:11777","ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology, 2022."},"date_published":"2022-08-11T00:00:00Z","day":"11","has_accepted_license":"1","article_processing_charge":"No","title":"High-dimensional expansion and crossing numbers of simplicial complexes","ddc":["500","516","514"],"status":"public","_id":"11777","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"date_updated":"2022-08-10T15:34:04Z","date_created":"2022-08-10T15:34:04Z","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","file_id":"11780","relation":"supplementary_material","creator":"pwild","file_size":16828,"content_type":"text/x-python","file_name":"flags.py","description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","access_level":"open_access"},{"relation":"supplementary_material","file_id":"11781","date_created":"2022-08-10T15:34:10Z","date_updated":"2022-08-10T15:34:10Z","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","file_name":"lowerbound.cpp","description":"Code for proof of Lemma 8.20 in Thesis","access_level":"open_access","file_size":12226,"content_type":"text/x-c++src","creator":"pwild"},{"date_updated":"2022-08-10T15:34:17Z","date_created":"2022-08-10T15:34:17Z","checksum":"4cf81455c49e5dec3b9b2e3980137eeb","relation":"supplementary_material","file_id":"11782","content_type":"text/x-python","file_size":3240,"creator":"pwild","description":"Code for proof of Proposition 7.9 in Thesis","file_name":"upperbound.py","access_level":"open_access"},{"creator":"pwild","content_type":"application/pdf","file_size":5086282,"access_level":"open_access","file_name":"finalthesisPascalWildPDFA.pdf","checksum":"4e96575b10cbe4e0d0db2045b2847774","date_updated":"2022-08-11T16:08:33Z","date_created":"2022-08-11T16:08:33Z","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","file_id":"11809","relation":"main_file"},{"access_level":"closed","file_name":"ThesisSubmission.zip","file_size":18150068,"content_type":"application/zip","creator":"pwild","relation":"source_file","file_id":"11810","checksum":"92d94842a1fb6dca5808448137573b2e","date_updated":"2022-08-11T16:09:19Z","date_created":"2022-08-11T16:09:19Z"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise.","lang":"eng"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"degree_awarded":"PhD","supervisor":[{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11777","month":"08","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-021-3"]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"publisher":"Institute of Science and Technology","year":"2022","date_created":"2022-08-10T15:51:19Z","date_updated":"2023-06-22T09:56:36Z","author":[{"id":"4C20D868-F248-11E8-B48F-1D18A9856A87","first_name":"Pascal","last_name":"Wild","full_name":"Wild, Pascal"}],"file_date_updated":"2022-08-11T16:09:19Z","ec_funded":1},{"file_date_updated":"2022-04-07T08:11:51Z","author":[{"full_name":"Matejovicova, Lenka","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87","last_name":"Matejovicova","first_name":"Lenka"}],"date_created":"2022-04-07T08:19:54Z","date_updated":"2023-06-23T06:26:41Z","year":"2022","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"month":"04","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-016-9"]},"doi":"10.15479/at:ista:11128","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"supervisor":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_name":"LenkaPhD_Official_PDFA.pdf","access_level":"open_access","file_size":11906472,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"11129","date_created":"2022-04-07T08:11:34Z","date_updated":"2022-04-07T08:11:34Z","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7"},{"access_level":"closed","file_name":"LenkaPhD Official_source.zip","creator":"cchlebak","content_type":"application/x-zip-compressed","file_size":23036766,"file_id":"11130","relation":"source_file","checksum":"99d67040432fd07a225643a212ee8588","date_updated":"2022-04-07T08:11:51Z","date_created":"2022-04-07T08:11:51Z"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11128","status":"public","ddc":["576","582"],"title":"Genetic basis of flower colour as a model for adaptive evolution","day":"06","article_processing_charge":"No","has_accepted_license":"1","date_published":"2022-04-06T00:00:00Z","citation":{"ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","apa":"Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128","chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128.","mla":"Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022."},"page":"112"},{"date_published":"2022-08-23T00:00:00Z","page":"133","citation":{"mla":"Schulz, Rouven. Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11945.","short":"R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022.","chicago":"Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11945.","ama":"Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. 2022. doi:10.15479/at:ista:11945","ista":"Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria.","ieee":"R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022.","apa":"Schulz, R. (2022). Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11945"},"day":"23","has_accepted_license":"1","article_processing_charge":"No","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"11970","checksum":"61b1b666a210ff7cdd0e95ea75207a13","success":1,"date_created":"2022-08-25T08:59:57Z","date_updated":"2022-08-25T08:59:57Z","access_level":"open_access","file_name":"Thesis_Rouven_Schulz_2022_final.pdf","file_size":28079331,"content_type":"application/pdf","creator":"rschulz"},{"checksum":"2b8f95ea1c134dbdb927b41b1dbeeeb5","date_created":"2022-08-25T09:00:11Z","date_updated":"2022-08-25T09:33:31Z","file_id":"11971","relation":"source_file","creator":"rschulz","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":27226963,"access_level":"closed","file_name":"Thesis_Rouven_Schulz_2022_final.docx"}],"title":"Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function","ddc":["570"],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11945","abstract":[{"text":"G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"supervisor":[{"first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11945","project":[{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"08","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-08-03T13:02:26Z","date_created":"2022-08-23T11:33:11Z","author":[{"full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz","first_name":"Rouven"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11995"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"publisher":"Institute of Science and Technology Austria","year":"2022","file_date_updated":"2022-08-25T09:33:31Z"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12390","title":"Translation-invariant quantum systems with effectively broken symmetry","status":"public","ddc":["500"],"oa_version":"Published Version","file":[{"file_name":"Brooks_Thesis.pdf","access_level":"open_access","file_size":3095225,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"12391","date_updated":"2023-01-26T10:02:34Z","date_created":"2023-01-26T10:02:34Z","checksum":"b31460e937f33b557abb40ebef02b567","success":1},{"relation":"source_file","file_id":"12392","checksum":"9751869fa5e7981588ad4228f4fd4bd6","date_updated":"2023-01-26T10:02:42Z","date_created":"2023-01-26T10:02:42Z","access_level":"closed","file_name":"Brooks_Thesis.tex","content_type":"application/octet-stream","file_size":809842,"creator":"cchlebak"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n"}],"citation":{"mla":"Brooks, Morris. Translation-Invariant Quantum Systems with Effectively Broken Symmetry. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12390.","short":"M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022.","chicago":"Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively Broken Symmetry.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12390.","ama":"Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:10.15479/at:ista:12390","ista":"Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria.","ieee":"M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022.","apa":"Brooks, M. (2022). Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12390"},"page":"196","date_published":"2022-12-15T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"15","year":"2022","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publication_status":"published","related_material":{"record":[{"id":"9005","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Brooks, Morris","orcid":"0000-0002-6249-0928","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","last_name":"Brooks","first_name":"Morris"}],"date_updated":"2023-08-07T13:32:09Z","date_created":"2023-01-26T10:00:42Z","ec_funded":1,"file_date_updated":"2023-01-26T10:02:42Z","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"doi":"10.15479/at:ista:12390","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"publication_identifier":{"issn":["2663-337X"]},"month":"12"},{"publication_identifier":{"isbn":[" 978-3-99078-025-1 "],"issn":["2663-337X"]},"month":"09","project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"doi":"10.15479/at:ista:12153","ec_funded":1,"file_date_updated":"2023-01-25T10:52:46Z","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2022","date_created":"2023-01-25T10:43:24Z","date_updated":"2023-08-08T13:14:10Z","related_material":{"record":[{"id":"9350","status":"public","relation":"part_of_dissertation"}]},"author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","first_name":"Feyza N","last_name":"Arslan","full_name":"Arslan, Feyza N"}],"has_accepted_license":"1","article_processing_charge":"No","day":"29","page":"113","citation":{"short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows, Institute of Science and Technology Austria, 2022.","mla":"Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153.","chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical flows. 2022. doi:10.15479/at:ista:12153","apa":"Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical flows,” Institute of Science and Technology Austria, 2022.","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria."},"date_published":"2022-09-29T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\u0002mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\u0002cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts.","lang":"eng"}],"title":"Remodeling of E-cadherin-mediated contacts via cortical flows","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12368","file":[{"file_id":"12369","relation":"main_file","date_created":"2023-01-25T10:52:46Z","date_updated":"2023-01-25T10:52:46Z","success":1,"checksum":"e54a3e69b83ebf166544164afd25608e","file_name":"THESIS_FINAL_FArslan_pdfa.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":14581024}],"oa_version":"Published Version"},{"year":"2022","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias"}],"related_material":{"record":[{"id":"10665","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10667"},{"id":"11366","relation":"part_of_dissertation","status":"public"},{"id":"7808","status":"public","relation":"part_of_dissertation"},{"id":"10666","relation":"part_of_dissertation","status":"public"}]},"date_created":"2022-05-12T07:14:01Z","date_updated":"2023-08-17T06:58:38Z","file_date_updated":"2022-05-17T15:19:39Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"doi":"10.15479/at:ista:11362","supervisor":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"isbn":["978-3-99078-017-6"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11362","status":"public","ddc":["004"],"title":"Learning verifiable representations","file":[{"file_size":13210143,"content_type":"application/zip","creator":"mlechner","file_name":"src.zip","access_level":"closed","date_updated":"2022-05-13T12:49:00Z","date_created":"2022-05-13T12:33:26Z","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","relation":"source_file","file_id":"11378"},{"content_type":"application/pdf","file_size":2732536,"creator":"mlechner","access_level":"open_access","file_name":"thesis_main-a2.pdf","checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","date_created":"2022-05-16T08:02:28Z","date_updated":"2022-05-17T15:19:39Z","relation":"main_file","file_id":"11382"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks.","lang":"eng"}],"citation":{"chicago":"Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362.","mla":"Lechner, Mathias. Learning Verifiable Representations. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11362.","short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria.","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022.","apa":"Lechner, M. (2022). Learning verifiable representations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11362","ama":"Lechner M. Learning verifiable representations. 2022. doi:10.15479/at:ista:11362"},"page":"124","date_published":"2022-05-12T00:00:00Z","keyword":["neural networks","verification","machine learning"],"day":"12","article_processing_charge":"No","has_accepted_license":"1"},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","citation":{"apa":"Mysliwy, K. (2022). Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11473","ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.","ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria.","ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:10.15479/at:ista:11473","chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11473.","short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","mla":"Mysliwy, Krzysztof. Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11473."},"page":"138","date_published":"2022-07-01T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"11473","status":"public","ddc":["515","539"],"title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","file":[{"date_created":"2022-07-05T08:12:56Z","date_updated":"2022-07-05T08:12:56Z","checksum":"7970714a20a6052f75fb27a6c3e9976e","success":1,"relation":"main_file","file_id":"11486","file_size":1830973,"content_type":"application/pdf","creator":"kmysliwy","file_name":"thes1_no_isbn_2_1b.pdf","access_level":"open_access"},{"date_updated":"2022-07-05T08:17:12Z","date_created":"2022-07-05T08:15:52Z","checksum":"647a2011fdf56277096c9350fefe1097","relation":"source_file","file_id":"11487","file_size":5831060,"content_type":"application/zip","creator":"kmysliwy","file_name":"thes_source.zip","access_level":"closed"}],"oa_version":"Published Version","month":"07","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:11473","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"SSU"}],"supervisor":[{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"language":[{"iso":"eng"}],"file_date_updated":"2022-07-05T08:17:12Z","ec_funded":1,"year":"2022","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"author":[{"full_name":"Mysliwy, Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof","last_name":"Mysliwy"}],"related_material":{"record":[{"id":"10564","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8705"}]},"date_created":"2022-06-30T12:15:03Z","date_updated":"2023-09-07T13:43:52Z"},{"month":"03","publication_identifier":{"isbn":["978-3-99078-015-2"],"issn":["2663-337X"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"oa":1,"supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10799","file_date_updated":"2022-03-10T12:11:48Z","ec_funded":1,"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","year":"2022","date_updated":"2023-10-17T12:31:54Z","date_created":"2022-02-28T13:03:49Z","author":[{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","first_name":"Nikola H","full_name":"Konstantinov, Nikola H"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8724"},{"relation":"part_of_dissertation","status":"public","id":"10803"},{"id":"10802","relation":"part_of_dissertation","status":"public"},{"id":"6590","status":"public","relation":"part_of_dissertation"}]},"keyword":["robustness","fairness","machine learning","PAC learning","adversarial learning"],"day":"08","article_processing_charge":"No","has_accepted_license":"1","page":"176","citation":{"ama":"Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:10.15479/at:ista:10799","apa":"Konstantinov, N. H. (2022). Robustness and fairness in machine learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10799","ieee":"N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute of Science and Technology Austria, 2022.","ista":"Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute of Science and Technology Austria.","short":"N.H. Konstantinov, Robustness and Fairness in Machine Learning, Institute of Science and Technology Austria, 2022.","mla":"Konstantinov, Nikola H. Robustness and Fairness in Machine Learning. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10799.","chicago":"Konstantinov, Nikola H. “Robustness and Fairness in Machine Learning.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10799."},"date_published":"2022-03-08T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Because of the increasing popularity of machine learning methods, it is becoming important to understand the impact of learned components on automated decision-making systems and to guarantee that their consequences are beneficial to society. In other words, it is necessary to ensure that machine learning is sufficiently trustworthy to be used in real-world applications. This thesis studies two properties of machine learning models that are highly desirable for the\r\nsake of reliability: robustness and fairness. In the first part of the thesis we study the robustness of learning algorithms to training data corruption. Previous work has shown that machine learning models are vulnerable to a range\r\nof training set issues, varying from label noise through systematic biases to worst-case data manipulations. This is an especially relevant problem from a present perspective, since modern machine learning methods are particularly data hungry and therefore practitioners often have to rely on data collected from various external sources, e.g. from the Internet, from app users or via crowdsourcing. Naturally, such sources vary greatly in the quality and reliability of the\r\ndata they provide. With these considerations in mind, we study the problem of designing machine learning algorithms that are robust to corruptions in data coming from multiple sources. We show that, in contrast to the case of a single dataset with outliers, successful learning within this model is possible both theoretically and practically, even under worst-case data corruptions. The second part of this thesis deals with fairness-aware machine learning. There are multiple areas where machine learning models have shown promising results, but where careful considerations are required, in order to avoid discrimanative decisions taken by such learned components. Ensuring fairness can be particularly challenging, because real-world training datasets are expected to contain various forms of historical bias that may affect the learning process. In this thesis we show that data corruption can indeed render the problem of achieving fairness impossible, by tightly characterizing the theoretical limits of fair learning under worst-case data manipulations. However, assuming access to clean data, we also show how fairness-aware learning can be made practical in contexts beyond binary classification, in particular in the challenging learning to rank setting."}],"ddc":["000"],"status":"public","title":"Robustness and fairness in machine learning","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10799","oa_version":"Published Version","file":[{"creator":"nkonstan","content_type":"application/pdf","file_size":4204905,"access_level":"open_access","file_name":"thesis.pdf","success":1,"checksum":"626bc523ae8822d20e635d0e2d95182e","date_created":"2022-03-06T11:42:54Z","date_updated":"2022-03-06T11:42:54Z","file_id":"10823","relation":"main_file"},{"access_level":"closed","file_name":"thesis.zip","file_size":22841103,"content_type":"application/x-zip-compressed","creator":"nkonstan","relation":"source_file","file_id":"10824","checksum":"e2ca2b88350ac8ea1515b948885cbcb1","date_created":"2022-03-06T11:42:57Z","date_updated":"2022-03-10T12:11:48Z"}]},{"day":"20","has_accepted_license":"1","article_processing_charge":"No","date_published":"2022-07-20T00:00:00Z","page":"248","citation":{"mla":"Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11626.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11626.","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","apa":"Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11626"},"abstract":[{"text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"content_type":"application/pdf","file_size":9730864,"creator":"mgallei","access_level":"open_access","file_name":"Thesis_Gallei.pdf","checksum":"bd7ac35403cf5b4b2607287d2a104b3a","date_created":"2022-07-25T09:08:47Z","date_updated":"2022-07-25T09:08:47Z","relation":"main_file","file_id":"11645"},{"access_level":"closed","file_name":"Thesis_Gallei_source.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":19560720,"creator":"mgallei","relation":"source_file","file_id":"11646","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","date_updated":"2022-07-25T09:39:58Z","date_created":"2022-07-25T09:09:09Z"},{"access_level":"closed","description":"This is the print version of the thesis including the full appendix","file_name":"Thesis_Gallei_to_print.pdf","content_type":"application/pdf","file_size":24542837,"creator":"mgallei","relation":"source_file","file_id":"11647","checksum":"3994f7f20058941b5bb8a16886b21e71","date_updated":"2022-07-25T09:39:58Z","date_created":"2022-07-25T09:09:32Z"},{"access_level":"open_access","file_name":"Thesis_Gallei_Appendix.pdf","content_type":"application/pdf","file_size":15435966,"creator":"mgallei","relation":"main_file","file_id":"11650","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","date_created":"2022-07-25T11:48:45Z","date_updated":"2022-07-25T11:48:45Z"}],"oa_version":"Published Version","status":"public","title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","ddc":["575"],"_id":"11626","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"07","publication_identifier":{"isbn":["978-3-99078-019-0"],"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eilon","last_name":"Shani","full_name":"Shani, Eilon"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11626","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"oa":1,"file_date_updated":"2022-07-25T11:48:45Z","ec_funded":1,"date_created":"2022-07-20T11:21:53Z","date_updated":"2023-11-07T08:20:13Z","author":[{"full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","first_name":"Michelle C"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8931"},{"status":"public","relation":"part_of_dissertation","id":"9287"},{"id":"7142","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"7465"},{"id":"8138","relation":"part_of_dissertation","status":"public"},{"id":"6260","status":"public","relation":"part_of_dissertation"},{"id":"10411","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"year":"2022"},{"year":"2022","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11736"},{"id":"9818","relation":"part_of_dissertation","status":"public"},{"id":"8385","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Georg","last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","full_name":"Sperl, Georg"}],"date_updated":"2024-02-28T12:57:46Z","date_created":"2023-01-24T10:49:46Z","ec_funded":1,"file_date_updated":"2023-02-02T09:39:25Z","oa":1,"project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:12103","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"publication_identifier":{"isbn":["978-3-99078-020-6"],"issn":["2663-337X"]},"month":"09","_id":"12358","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","ddc":["000","620"],"status":"public","file":[{"file_id":"12371","title":"Thesis","relation":"main_file","checksum":"083722acbb8115e52e3b0fdec6226769","date_updated":"2023-02-02T09:29:57Z","date_created":"2023-01-25T12:04:41Z","access_level":"open_access","file_name":"thesis_gsperl.pdf","description":"This is the main PDF file of the thesis. File size: 105 MB","creator":"cchlebak","content_type":"application/pdf","file_size":104497530},{"content_type":"application/pdf","file_size":23183710,"creator":"cchlebak","file_name":"thesis_gsperl_compressed.pdf","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","access_level":"open_access","date_created":"2023-02-02T09:33:37Z","date_updated":"2023-02-02T09:33:37Z","checksum":"511f82025e5fcb70bff4731d6896ca07","relation":"main_file","file_id":"12483","title":"Thesis (compressed 23MB)"},{"file_name":"thesis-source.zip","access_level":"open_access","creator":"cchlebak","content_type":"application/x-zip-compressed","file_size":98382247,"file_id":"12484","relation":"source_file","date_created":"2023-02-02T09:39:25Z","date_updated":"2023-02-02T09:39:25Z","checksum":"ed4cb85225eedff761c25bddfc37a2ed"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n","lang":"eng"}],"citation":{"chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12103.","mla":"Sperl, Georg. Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12103.","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","apa":"Sperl, G. (2022). Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12103","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:10.15479/at:ista:12103"},"page":"138","date_published":"2022-09-22T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"22"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10759","ddc":["530"],"status":"public","title":"Analytic and machine learning approaches to composite quantum impurities","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"10785","date_updated":"2022-02-22T07:20:12Z","date_created":"2022-02-21T13:58:16Z","checksum":"0fc54ad1eaede879c665ac9b53c93e22","file_name":"Rzadkowski_thesis_final_source.zip","access_level":"closed","file_size":17668233,"content_type":"application/zip","creator":"wrzadkow"},{"file_size":13307331,"content_type":"application/pdf","creator":"wrzadkow","access_level":"open_access","file_name":"Rzadkowski_thesis_final.pdf","checksum":"22d2d7af37ca31f6b1730c26cac7bced","success":1,"date_updated":"2022-02-21T14:02:54Z","date_created":"2022-02-21T14:02:54Z","relation":"main_file","file_id":"10786"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data."}],"citation":{"ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","apa":"Rzadkowski, W. (2022). Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759","ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria.","ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:10.15479/at:ista:10759","chicago":"Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759.","short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022.","mla":"Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759."},"page":"120","date_published":"2022-02-21T00:00:00Z","day":"21","article_processing_charge":"No","has_accepted_license":"1","year":"2022","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"author":[{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1106-4419","first_name":"Wojciech","last_name":"Rzadkowski","full_name":"Rzadkowski, Wojciech"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10762"},{"id":"8644","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7956"},{"id":"415","relation":"part_of_dissertation","status":"public"}]},"date_created":"2022-02-16T13:27:37Z","date_updated":"2024-02-28T13:01:59Z","file_date_updated":"2022-02-22T07:20:12Z","ec_funded":1,"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"doi":"10.15479/at:ista:10759","degree_awarded":"PhD","supervisor":[{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"}],"language":[{"iso":"eng"}],"month":"02","publication_identifier":{"issn":["2663-337X"]}},{"doi":"10.15479/at:ista:11196","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"project":[{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","grant_number":"708497","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","call_identifier":"H2020"},{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"grant_number":"W01205","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Zellkommunikation in Gesundheit und Krankheit"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"publication_identifier":{"issn":["2663-337X"]},"month":"04","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11222"},{"relation":"part_of_dissertation","status":"public","id":"7473"}]},"author":[{"last_name":"Kim","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Olena"}],"date_updated":"2023-08-18T06:31:52Z","date_created":"2022-04-20T09:47:12Z","year":"2022","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","ec_funded":1,"file_date_updated":"2023-04-20T22:30:03Z","date_published":"2022-04-20T00:00:00Z","citation":{"short":"O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022.","mla":"Kim, Olena. Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11196.","chicago":"Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11196.","ama":"Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. 2022. doi:10.15479/at:ista:11196","ieee":"O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022.","apa":"Kim, O. (2022). Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11196","ista":"Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria."},"page":"132","has_accepted_license":"1","article_processing_charge":"No","day":"20","oa_version":"Published Version","file":[{"creator":"okim","file_size":21273537,"content_type":"application/pdf","file_name":"Olena_KIM_thesis_final.pdf","access_level":"open_access","date_created":"2022-04-20T14:21:56Z","date_updated":"2023-04-20T22:30:03Z","checksum":"1616a8bf6f13a57c892dac873dcd0936","embargo":"2023-04-19","file_id":"11220","relation":"main_file"},{"file_id":"11221","relation":"source_file","checksum":"1acb433f98dc42abb0b4b0cbb0c4b918","date_updated":"2023-04-20T22:30:03Z","date_created":"2022-04-20T14:22:56Z","access_level":"closed","file_name":"KIM_thesis_final.zip","embargo_to":"open_access","creator":"okim","content_type":"application/x-zip-compressed","file_size":59248569}],"_id":"11196","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses","ddc":["570"],"abstract":[{"lang":"eng","text":"One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n"}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"oa_version":"Published Version","file":[{"date_created":"2022-02-04T15:36:12Z","date_updated":"2023-02-03T23:30:03Z","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","relation":"source_file","file_id":"10728","file_size":6757886,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"smetzler","embargo_to":"open_access","file_name":"Thesis_Sina_Metzler.docx","access_level":"closed"},{"creator":"smetzler","content_type":"application/pdf","file_size":6314921,"access_level":"open_access","file_name":"Thesis_Sina_Metzler_A2.pdf","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","date_updated":"2023-02-03T23:30:03Z","date_created":"2022-02-04T15:36:43Z","file_id":"10730","embargo":"2023-02-02","relation":"main_file"},{"creator":"smetzler","content_type":"application/pdf","file_size":6882557,"file_name":"Thesis_Sina_Metzler_print.pdf","access_level":"open_access","date_created":"2022-02-07T10:35:02Z","date_updated":"2023-02-04T23:30:03Z","checksum":"dedd14b7be7a75d63018dbfc68dd8113","file_id":"10742","embargo":"2023-02-02","relation":"main_file"}],"_id":"10727","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Pathogen-mediated sexual selection and immunization in ant colonies","ddc":["570"],"status":"public","abstract":[{"text":"Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).\r\nIn the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.\r\nIn the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.\r\nFirst, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2022-02-07T00:00:00Z","citation":{"chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10727.","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","mla":"Metzler, Sina. Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10727.","ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022.","apa":"Metzler, S. (2022). Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10727","ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria.","ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:10.15479/AT:ISTA:10727"},"day":"07","has_accepted_license":"1","article_processing_charge":"No","author":[{"full_name":"Metzler, Sina","first_name":"Sina","last_name":"Metzler","id":"48204546-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9547-2494"}],"date_created":"2022-02-04T15:45:12Z","date_updated":"2023-09-07T13:43:23Z","year":"2022","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"file_date_updated":"2023-02-04T23:30:03Z","ec_funded":1,"doi":"10.15479/AT:ISTA:10727","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"}],"supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"month":"02","publication_identifier":{"issn":["2663-337X"]}},{"file_date_updated":"2023-09-09T22:30:03Z","year":"2022","acknowledgement":"I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02).","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","author":[{"full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina","last_name":"Artner"}],"date_updated":"2023-09-09T22:30:04Z","date_created":"2022-08-17T07:58:53Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-022-0"]},"month":"08","oa":1,"project":[{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:11879","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"degree_awarded":"PhD","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT.","lang":"eng"}],"_id":"11879","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","status":"public","ddc":["580"],"file":[{"file_size":11113608,"content_type":"application/pdf","creator":"cartner","file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","access_level":"open_access","date_created":"2022-08-17T12:08:49Z","date_updated":"2023-09-09T22:30:03Z","checksum":"a2c2fdc28002538840490bfa6a08b2cb","relation":"main_file","embargo":"2023-09-08","file_id":"11907"},{"access_level":"closed","file_name":"ChristinaArtner_PhD_Thesis_2022.7z","embargo_to":"open_access","creator":"cartner","file_size":19097730,"content_type":"application/octet-stream","file_id":"11908","relation":"source_file","checksum":"66b461c074b815fbe63481b3f46a9f43","date_created":"2022-08-17T12:08:59Z","date_updated":"2023-09-09T22:30:03Z"}],"oa_version":"Published Version","keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"has_accepted_license":"1","article_processing_charge":"No","day":"17","citation":{"ama":"Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:10.15479/at:ista:11879","ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022.","apa":"Artner, C. (2022). Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11879","mla":"Artner, Christina. Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11879.","short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022.","chicago":"Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11879."},"page":"128","date_published":"2022-08-17T00:00:00Z"},{"article_processing_charge":"No","has_accepted_license":"1","day":"16","page":"108","citation":{"chicago":"Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11393.","short":"M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology Austria, 2022.","mla":"Jevtic, Marijo. Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11393.","apa":"Jevtic, M. (2022). Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11393","ieee":"M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus,” Institute of Science and Technology Austria, 2022.","ista":"Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria.","ama":"Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:10.15479/at:ista:11393"},"date_published":"2022-05-16T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is\r\nimplicated in complex processes such as learning and memory and various neurological\r\ndiseases. These receptors are composed of different subunits and the subunit composition can\r\naffect channel properties, receptor trafficking and interaction with other associated proteins.\r\nUsing the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus. I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those\r\nfor other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity and particular contribution of different\r\nAMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings\r\nfurther contribute to our understanding of how specific hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit composition at the single\r\nchannel level in situ have been available. Electron microscopy with conventional immunogold\r\nlabeling approaches has limitations in the single channel analysis because of the large size of\r\nantibodies and steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to\r\nproteins of interest (reactive tag system). I additionally made substantial progress into adapting\r\nthis system for AMPA receptor subunits.","lang":"eng"}],"ddc":["570"],"status":"public","title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11393","file":[{"access_level":"closed","file_name":"MJ thesis.docx","embargo_to":"open_access","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":56427603,"file_id":"11395","relation":"source_file","checksum":"8fc695d88020d70d231dad0e9f10b138","date_created":"2022-05-17T09:08:06Z","date_updated":"2023-05-17T22:30:03Z"},{"embargo":"2023-05-16","file_id":"11397","relation":"main_file","checksum":"c1dd20a1aece521b3500607b00e463d6","date_updated":"2023-05-17T22:30:03Z","date_created":"2022-05-17T12:09:25Z","access_level":"open_access","file_name":"MJ_thesis_PDFA.pdf","creator":"cchlebak","file_size":4351981,"content_type":"application/pdf"}],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"month":"05","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.15479/at:ista:11393","file_date_updated":"2023-05-17T22:30:03Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2022","date_updated":"2023-09-07T14:53:44Z","date_created":"2022-05-17T08:57:41Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7391"}]},"author":[{"full_name":"Jevtic, Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","last_name":"Jevtic","first_name":"Marijo"}]},{"_id":"12366","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Controllable states of superconducting Qubit ensembles","status":"public","ddc":["530"],"oa_version":"Published Version","file":[{"file_id":"12367","embargo":"2022-12-28","relation":"main_file","date_created":"2023-01-25T09:41:49Z","date_updated":"2023-01-26T23:30:44Z","checksum":"39eabb1e006b41335f17f3b29af09648","file_name":"Final_Thesis_ES_Redchenko.pdf","access_level":"open_access","creator":"cchlebak","file_size":56076868,"content_type":"application/pdf"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n"}],"citation":{"mla":"Redchenko, Elena. Controllable States of Superconducting Qubit Ensembles. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12132.","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022.","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12132.","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:10.15479/at:ista:12132","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","apa":"Redchenko, E. (2022). Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12132"},"page":"168","date_published":"2022-09-26T00:00:00Z","day":"26","article_processing_charge":"No","has_accepted_license":"1","year":"2022","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"author":[{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena"}],"date_created":"2023-01-25T09:17:02Z","date_updated":"2023-05-26T09:29:07Z","file_date_updated":"2023-01-26T23:30:44Z","ec_funded":1,"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","call_identifier":"H2020"}],"doi":"10.15479/at:ista:12132","supervisor":[{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"isbn":["978-3-99078-024-4"],"issn":["2663-337X"]}},{"_id":"11932","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"On the encoding, transfer, and consolidation of spatial memories","status":"public","ddc":["573"],"file":[{"relation":"source_file","file_id":"11935","date_updated":"2023-06-20T22:30:04Z","date_created":"2022-08-19T16:31:34Z","checksum":"2dbb70c74aaa3b64c1f463e943baf09c","embargo_to":"open_access","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","access_level":"closed","file_size":13515457,"content_type":"application/zip","creator":"mnardin"},{"date_created":"2022-08-22T09:43:50Z","date_updated":"2023-06-20T22:30:04Z","checksum":"0ec94035ea35a47a9f589ed168e60b48","embargo":"2023-06-19","file_id":"11941","relation":"main_file","creator":"mnardin","file_size":9906458,"content_type":"application/pdf","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes.","lang":"eng"}],"citation":{"ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:10.15479/at:ista:11932","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria.","apa":"Nardin, M. (2022). On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11932","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","mla":"Nardin, Michele. On the Encoding, Transfer, and Consolidation of Spatial Memories. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11932.","short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11932."},"page":"136","date_published":"2022-08-19T00:00:00Z","day":"19","has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2022","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"author":[{"full_name":"Nardin, Michele","first_name":"Michele","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570"}],"related_material":{"record":[{"id":"10077","status":"public","relation":"part_of_dissertation"},{"id":"6194","status":"public","relation":"part_of_dissertation"}]},"date_created":"2022-08-19T08:52:30Z","date_updated":"2023-09-05T12:02:14Z","file_date_updated":"2023-06-20T22:30:04Z","ec_funded":1,"oa":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:11932","degree_awarded":"PhD","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["2663-337X"]}},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia."}],"status":"public","title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12378","oa_version":"Published Version","file":[{"file_id":"12379","relation":"source_file","date_updated":"2023-04-12T22:30:03Z","date_created":"2023-01-25T14:31:32Z","checksum":"8cd3ddfe9b53381dcf086023d8d8893a","file_name":"Gloria_Colombo_Thesis.docx","embargo_to":"open_access","access_level":"closed","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":23890382},{"creator":"cchlebak","file_size":13802421,"content_type":"application/pdf","access_level":"open_access","file_name":"Gloria_Colombo_Thesis.pdf","checksum":"8af4319c18b516e8758e9a6cb02b103b","date_created":"2023-01-25T14:31:36Z","date_updated":"2023-04-12T22:30:03Z","file_id":"12380","embargo":"2023-04-11","relation":"main_file"}],"day":"11","article_processing_charge":"No","has_accepted_license":"1","page":"142","citation":{"chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12378.","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","mla":"Colombo, Gloria. MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12378.","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022.","apa":"Colombo, G. (2022). MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12378","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:10.15479/at:ista:12378"},"date_published":"2022-11-11T00:00:00Z","file_date_updated":"2023-04-12T22:30:03Z","ec_funded":1,"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"publisher":"Institute of Science and Technology Austria","year":"2022","date_created":"2023-01-25T14:27:43Z","date_updated":"2023-08-04T09:40:37Z","author":[{"full_name":"Colombo, Gloria","last_name":"Colombo","first_name":"Gloria","orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"12244","status":"public","relation":"part_of_dissertation"}]},"month":"11","publication_identifier":{"issn":["2663-337X"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"supervisor":[{"first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12378"},{"day":"18","article_processing_charge":"No","has_accepted_license":"1","date_published":"2022-05-18T00:00:00Z","page":"98","citation":{"ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","apa":"Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","mla":"Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388.","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388."},"abstract":[{"lang":"eng","text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"checksum":"4d75e6a619df7e8a9d6e840aee182380","date_created":"2022-05-19T13:03:13Z","date_updated":"2023-05-20T22:30:03Z","file_id":"11398","embargo":"2023-05-19","relation":"main_file","creator":"sbelohla","file_size":8247240,"content_type":"application/pdf","access_level":"open_access","file_name":"thesis_sb_final_pdfa.pdf"},{"file_name":"thesis_sb_final.zip","embargo_to":"open_access","access_level":"closed","creator":"sbelohla","content_type":"application/x-zip-compressed","file_size":7094,"file_id":"11399","relation":"source_file","date_created":"2022-05-19T13:07:47Z","date_updated":"2023-05-20T22:30:03Z","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0"}],"oa_version":"Published Version","title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","status":"public","ddc":["576"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11388","month":"05","publication_identifier":{"isbn":["978-3-99078-018-3"]},"supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11388","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2023-05-20T22:30:03Z","date_updated":"2023-08-29T06:41:51Z","date_created":"2022-05-16T16:49:18Z","author":[{"full_name":"Belohlavy, Stefanie","first_name":"Stefanie","last_name":"Belohlavy","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X"}],"related_material":{"record":[{"id":"6713","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","year":"2022"},{"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2022","date_created":"2023-01-26T11:55:16Z","date_updated":"2023-12-21T23:30:04Z","related_material":{"record":[{"id":"679","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10703"},{"relation":"part_of_dissertation","status":"public","id":"9429"},{"id":"7885","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Tasciyan, Saren","last_name":"Tasciyan","first_name":"Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-12-21T23:30:03Z","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:12401","publication_identifier":{"issn":["2663-337X"]},"month":"12","status":"public","ddc":["610"],"title":"Role of microenvironment heterogeneity in cancer cell invasion","_id":"12401","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"date_updated":"2023-12-21T23:30:03Z","date_created":"2023-01-26T11:58:14Z","checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd","embargo":"2023-12-20","file_id":"12402","relation":"main_file","creator":"cchlebak","file_size":42059787,"content_type":"application/pdf","file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","access_level":"open_access"},{"checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","date_created":"2023-01-26T12:00:10Z","date_updated":"2023-12-21T23:30:03Z","file_id":"12403","relation":"source_file","creator":"cchlebak","content_type":"application/x-zip-compressed","file_size":261256696,"access_level":"closed","file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","embargo_to":"open_access"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening.","lang":"eng"}],"page":"105","citation":{"ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:10.15479/at:ista:12401","ista":"Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria.","apa":"Tasciyan, S. (2022). Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12401","ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","mla":"Tasciyan, Saren. Role of Microenvironment Heterogeneity in Cancer Cell Invasion. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12401.","short":"S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022.","chicago":"Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12401."},"date_published":"2022-12-22T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"22"},{"abstract":[{"text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf","access_level":"open_access","file_size":8820951,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"11195","embargo":"2023-04-20","date_created":"2022-04-20T09:03:57Z","date_updated":"2023-04-21T22:30:03Z","checksum":"999ab16884c4522486136ebc5ae8dbff"},{"date_updated":"2023-04-21T22:30:03Z","date_created":"2022-04-22T12:41:00Z","checksum":"fd92b1e38d53bdf8b458213882d41383","file_id":"11329","relation":"source_file","creator":"cchlebak","content_type":"application/x-zip-compressed","file_size":65864612,"file_name":"Thesis_Stephanie_Wachner_20200414.zip","embargo_to":"open_access","access_level":"closed"}],"oa_version":"Published Version","title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells","status":"public","ddc":["570"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11193","day":"20","has_accepted_license":"1","article_processing_charge":"No","date_published":"2022-04-20T00:00:00Z","page":"170","citation":{"ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:10.15479/at:ista:11193","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria.","apa":"Wachner, S. (2022). Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11193","ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022.","mla":"Wachner, Stephanie. Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11193.","short":"S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022.","chicago":"Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11193."},"file_date_updated":"2023-04-21T22:30:03Z","date_created":"2022-04-20T08:59:07Z","date_updated":"2023-09-19T10:15:54Z","author":[{"full_name":"Wachner, Stephanie","last_name":"Wachner","first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"10614","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"544"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"DaSi"}],"publisher":"Institute of Science and Technology Austria","year":"2022","month":"04","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"}],"supervisor":[{"orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E","full_name":"Siekhaus, Daria E"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11193","project":[{"_id":"26199CA4-B435-11E9-9278-68D0E5697425","grant_number":"24800","name":"Tissue barrier penetration is crucial for immunity and metastasis"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"file_date_updated":"2023-09-20T22:30:03Z","ec_funded":1,"year":"2022","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","first_name":"Christoph","full_name":"Dotter, Christoph"}],"related_material":{"record":[{"id":"3","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"11160"}]},"date_created":"2023-01-24T13:09:57Z","date_updated":"2023-11-16T13:10:22Z","month":"09","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299","_id":"254BA948-B435-11E9-9278-68D0E5697425"},{"name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","grant_number":"707964"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020"},{"_id":"2690FEAC-B435-11E9-9278-68D0E5697425","grant_number":"I04205","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","call_identifier":"FWF"}],"doi":"10.15479/at:ista:12094","supervisor":[{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence.","lang":"eng"}],"_id":"12364","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","status":"public","ddc":["570"],"file":[{"access_level":"open_access","file_name":"220923_Thesis_CDotter_Final.pdf","file_size":20457465,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"12365","embargo":"2023-09-19","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","date_created":"2023-01-24T13:15:45Z","date_updated":"2023-09-20T22:30:03Z"},{"creator":"cchlebak","content_type":"application/x-zip-compressed","file_size":22433512,"file_name":"latex_source_CDotter_Thesis_2022.zip","embargo_to":"open_access","access_level":"closed","date_created":"2023-02-02T09:15:35Z","date_updated":"2023-09-20T22:30:03Z","checksum":"ad01bb20da163be6893b7af832e58419","file_id":"12482","relation":"source_file"}],"oa_version":"Published Version","day":"19","article_processing_charge":"No","has_accepted_license":"1","citation":{"short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","mla":"Dotter, Christoph. Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12094.","chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12094.","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:10.15479/at:ista:12094","apa":"Dotter, C. (2022). Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12094","ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.","ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria."},"page":"152","date_published":"2022-09-19T00:00:00Z"},{"place":"Klosterneuburg","file_date_updated":"2021-02-03T10:37:28Z","year":"2021","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"187","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8703"}]},"author":[{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F"}],"date_updated":"2023-09-07T13:29:01Z","date_created":"2021-02-02T14:11:06Z","publication_identifier":{"issn":["2663-337X"]},"month":"02","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"doi":"10.15479/AT:ISTA:9056","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"degree_awarded":"PhD","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9056","status":"public","title":"Multi-cover persistence and Delaunay mosaics","ddc":["006","514","516"],"oa_version":"Published Version","file":[{"file_name":"thesis_source.zip","access_level":"closed","file_size":13446994,"content_type":"application/zip","creator":"patrickd","relation":"source_file","file_id":"9063","date_created":"2021-02-02T14:09:25Z","date_updated":"2021-02-03T10:37:28Z","checksum":"bcf27986147cab0533b6abadd74e7629"},{"file_id":"9064","relation":"main_file","success":1,"checksum":"9cc8af266579a464385bbe2aff6af606","date_updated":"2021-02-02T14:09:18Z","date_created":"2021-02-02T14:09:18Z","access_level":"open_access","file_name":"thesis_pdfA2b.pdf","creator":"patrickd","file_size":5210329,"content_type":"application/pdf"}],"article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9056.","short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021.","mla":"Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056.","apa":"Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056"},"page":"134","date_published":"2021-02-01T00:00:00Z"},{"oa_version":"Published Version","file":[{"file_name":"thesis.pdf","access_level":"open_access","file_size":4127796,"content_type":"application/pdf","creator":"gcipollo","relation":"main_file","file_id":"9043","date_created":"2021-01-25T14:19:03Z","date_updated":"2021-01-25T14:19:03Z","checksum":"5a93658a5f19478372523ee232887e2b","success":1},{"access_level":"closed","file_name":"Thesis_files.zip","content_type":"application/zip","file_size":12775206,"creator":"gcipollo","relation":"source_file","file_id":"9044","checksum":"e8270eddfe6a988e92a53c88d1d19b8c","date_created":"2021-01-25T14:19:10Z","date_updated":"2021-01-25T14:19:10Z"}],"ddc":["510"],"status":"public","title":"Fluctuations in the spectrum of random matrices","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9022","abstract":[{"lang":"eng","text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2021-01-25T00:00:00Z","page":"380","citation":{"mla":"Cipolloni, Giorgio. Fluctuations in the Spectrum of Random Matrices. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9022.","short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9022.","ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:10.15479/AT:ISTA:9022","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria.","ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","apa":"Cipolloni, G. (2021). Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9022"},"day":"25","article_processing_charge":"No","has_accepted_license":"1","date_updated":"2023-09-07T13:29:32Z","date_created":"2021-01-21T18:16:54Z","author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","first_name":"Giorgio","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.","year":"2021","file_date_updated":"2021-01-25T14:19:10Z","ec_funded":1,"degree_awarded":"PhD","supervisor":[{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:9022","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"oa":1,"month":"01","publication_identifier":{"issn":["2663-337X"]}},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis.","lang":"eng"}],"status":"public","ddc":["515"],"title":"Curvature driven interface evolution: Uniqueness properties of weak solution concepts","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10007","oa_version":"Published Version","file":[{"creator":"shensel","content_type":"application/x-zip-compressed","file_size":15022154,"access_level":"closed","file_name":"thesis_final_Hensel.zip","checksum":"c8475faaf0b680b4971f638f1db16347","date_updated":"2021-09-15T14:37:30Z","date_created":"2021-09-13T11:03:24Z","file_id":"10008","relation":"source_file"},{"creator":"shensel","content_type":"application/pdf","file_size":6583638,"access_level":"open_access","file_name":"thesis_final_Hensel.pdf","checksum":"1a609937aa5275452822f45f2da17f07","date_updated":"2021-09-14T09:52:47Z","date_created":"2021-09-13T14:18:56Z","file_id":"10014","relation":"main_file"}],"day":"14","article_processing_charge":"No","has_accepted_license":"1","page":"300","citation":{"chicago":"Hensel, Sebastian. “Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10007.","mla":"Hensel, Sebastian. Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10007.","short":"S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts, Institute of Science and Technology Austria, 2021.","ista":"Hensel S. 2021. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria.","ieee":"S. Hensel, “Curvature driven interface evolution: Uniqueness properties of weak solution concepts,” Institute of Science and Technology Austria, 2021.","apa":"Hensel, S. (2021). Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10007","ama":"Hensel S. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. 2021. doi:10.15479/at:ista:10007"},"date_published":"2021-09-14T00:00:00Z","file_date_updated":"2021-09-15T14:37:30Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"year":"2021","date_updated":"2023-09-07T13:30:45Z","date_created":"2021-09-13T11:12:34Z","author":[{"first_name":"Sebastian","last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10012"},{"relation":"part_of_dissertation","status":"public","id":"10013"},{"id":"7489","status":"public","relation":"part_of_dissertation"}]},"month":"09","publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819","call_identifier":"H2020","name":"Bridging Scales in Random Materials"}],"oa":1,"degree_awarded":"PhD","supervisor":[{"full_name":"Fischer, Julian L","first_name":"Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10007"},{"ddc":["515"],"title":"Discrete-to-continuum limits of transport problems and gradient flows in the space of measures","status":"public","_id":"10030","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"source_file","file_id":"10032","date_created":"2021-09-21T09:17:34Z","date_updated":"2022-03-10T12:14:42Z","checksum":"8cd60dcb8762e8f21867e21e8001e183","file_name":"tex_and_pictures.zip","access_level":"closed","file_size":3876668,"content_type":"application/x-zip-compressed","creator":"cchlebak"},{"relation":"main_file","file_id":"10047","checksum":"9789e9d967c853c1503ec7f307170279","date_created":"2021-09-27T11:14:31Z","date_updated":"2021-09-27T11:14:31Z","access_level":"open_access","file_name":"thesis_portinale_Final (1).pdf","file_size":2532673,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning\r\nnon-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces."}],"citation":{"chicago":"Portinale, Lorenzo. “Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10030.","mla":"Portinale, Lorenzo. Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10030.","short":"L. Portinale, Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures, Institute of Science and Technology Austria, 2021.","ista":"Portinale L. 2021. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria.","apa":"Portinale, L. (2021). Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10030","ieee":"L. Portinale, “Discrete-to-continuum limits of transport problems and gradient flows in the space of measures,” Institute of Science and Technology Austria, 2021.","ama":"Portinale L. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. 2021. doi:10.15479/at:ista:10030"},"date_published":"2021-09-22T00:00:00Z","day":"22","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No W1245.","year":"2021","date_updated":"2023-09-07T13:31:06Z","date_created":"2021-09-21T09:14:15Z","author":[{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","first_name":"Lorenzo","full_name":"Portinale, Lorenzo"}],"related_material":{"record":[{"id":"10022","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9792"},{"id":"7573","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2022-03-10T12:14:42Z","project":[{"name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","full_name":"Maas, Jan"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10030","month":"09","publication_identifier":{"issn":["2663-337X"]}},{"file_date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-16T09:44:09Z","date_updated":"2023-09-07T13:31:22Z","related_material":{"record":[{"id":"9928","status":"public","relation":"part_of_dissertation"},{"id":"8755","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Peruzzo, Matilda","last_name":"Peruzzo","first_name":"Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","publication_identifier":{"isbn":["978-3-99078-013-8"],"issn":["2663-337X"]},"month":"08","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:9920","oa":1,"abstract":[{"text":"This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"checksum":"3cd1986efde5121d7581f6fcf9090da8","date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-16T09:33:21Z","relation":"source_file","file_id":"9924","content_type":"application/x-zip-compressed","file_size":151387283,"creator":"mperuzzo","access_level":"closed","file_name":"GeometricSuperinductorsForCQED.zip"},{"relation":"main_file","file_id":"9939","checksum":"50928c621cdf0775d7a5906b9dc8602c","date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-18T14:20:06Z","access_level":"open_access","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","content_type":"application/pdf","file_size":17596344,"creator":"mperuzzo"},{"date_created":"2021-08-18T14:20:09Z","date_updated":"2021-09-06T08:39:47Z","checksum":"37f486aa1b622fe44af00d627ec13f6c","relation":"other","file_id":"9940","file_size":17592425,"content_type":"application/pdf","creator":"mperuzzo","description":"Extra copy of the thesis as PDF/A-2b","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","access_level":"closed"}],"oa_version":"Published Version","title":"Geometric superinductors and their applications in circuit quantum electrodynamics","status":"public","ddc":["539"],"_id":"9920","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","has_accepted_license":"1","day":"19","keyword":["quantum computing","superinductor","quantum metrology"],"date_published":"2021-08-19T00:00:00Z","page":"149","citation":{"ama":"Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:10.15479/at:ista:9920","ieee":"M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021.","apa":"Peruzzo, M. (2021). Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9920","ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria.","short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021.","mla":"Peruzzo, Matilda. Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9920.","chicago":"Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9920."}},{"file_date_updated":"2022-03-10T12:10:25Z","abstract":[{"text":"Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Master's Thesis"],"author":[{"id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","first_name":"Anton","last_name":"Piankov","full_name":"Piankov, Anton"}],"date_updated":"2023-09-07T13:34:12Z","date_created":"2021-12-07T10:48:06Z","file":[{"file_name":"Thesis.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":394018,"creator":"cchlebak","relation":"source_file","file_id":"10424","date_created":"2021-12-07T11:13:52Z","date_updated":"2022-03-10T12:10:25Z","checksum":"114e8f4b2c002c6c352416c12de2c695"},{"checksum":"cd15ae991ced352a9959815f794e657c","date_created":"2021-12-07T11:14:01Z","date_updated":"2022-03-10T12:10:25Z","relation":"source_file","file_id":"10425","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":47638,"creator":"cchlebak","access_level":"closed","file_name":"Preliminary_pages_Piankov.docx"},{"file_name":"2021_Piankov_combined.pdf","access_level":"open_access","content_type":"application/pdf","file_size":484965,"creator":"cchlebak","relation":"main_file","file_id":"10426","date_created":"2021-12-07T11:20:35Z","date_updated":"2021-12-07T11:20:35Z","checksum":"e6899c798b75ba42fab9822bce309050","success":1}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10422","year":"2021","status":"public","title":"Towards designer materials using customizable particle shape","publication_status":"published","ddc":["530"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaGo"}],"month":"12","day":"07","article_processing_charge":"No","publication_identifier":{"issn":["2791-4585"]},"has_accepted_license":"1","date_published":"2021-12-07T00:00:00Z","doi":"10.15479/at:ista:10422","supervisor":[{"full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich"}],"degree_awarded":"MS","language":[{"iso":"eng"}],"citation":{"ama":"Piankov A. Towards designer materials using customizable particle shape. 2021. doi:10.15479/at:ista:10422","apa":"Piankov, A. (2021). Towards designer materials using customizable particle shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422","ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021.","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria.","short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021.","mla":"Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422.","chicago":"Piankov, Anton. “Towards Designer Materials Using Customizable Particle Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422."},"oa":1},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9418","title":"Underspecification in deep learning","status":"public","ddc":["000"],"oa_version":"Published Version","file":[{"file_size":2673905,"content_type":"application/pdf","creator":"bphuong","access_level":"open_access","file_name":"mph-thesis-v519-pdfimages.pdf","checksum":"4f0abe64114cfed264f9d36e8d1197e3","success":1,"date_updated":"2021-05-24T11:22:29Z","date_created":"2021-05-24T11:22:29Z","relation":"main_file","file_id":"9419"},{"file_name":"thesis.zip","access_level":"closed","file_size":92995100,"content_type":"application/zip","creator":"bphuong","relation":"source_file","file_id":"9420","date_created":"2021-05-24T11:56:02Z","date_updated":"2021-05-24T11:56:02Z","checksum":"f5699e876bc770a9b0df8345a77720a2"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models."}],"citation":{"ama":"Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","apa":"Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","mla":"Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418."},"page":"125","date_published":"2021-05-30T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"30","year":"2021","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"deleted","id":"7435"},{"status":"public","relation":"part_of_dissertation","id":"7481"},{"status":"public","relation":"part_of_dissertation","id":"9416"},{"id":"7479","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong","last_name":"Bui Thi Mai"}],"date_created":"2021-05-24T13:06:23Z","date_updated":"2023-09-08T11:11:12Z","file_date_updated":"2021-05-24T11:56:02Z","oa":1,"doi":"10.15479/AT:ISTA:9418","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"publication_identifier":{"issn":["2663-337X"]},"month":"05"},{"publication_identifier":{"issn":["2663-337X"]},"month":"10","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"SSU"}],"supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"doi":"10.15479/at:ista:10199","ec_funded":1,"file_date_updated":"2021-11-09T09:00:50Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","date_updated":"2023-09-19T09:59:54Z","date_created":"2021-10-29T20:09:01Z","related_material":{"record":[{"id":"10190","status":"public","relation":"part_of_dissertation"},{"id":"10191","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9987"},{"status":"public","relation":"part_of_dissertation","id":"141"}]},"author":[{"full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","first_name":"Viktor"}],"keyword":["concurrency","verification","model checking"],"has_accepted_license":"1","article_processing_charge":"No","day":"31","page":"166","citation":{"chicago":"Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10199.","short":"V. Toman, Improved Verification Techniques for Concurrent Systems, Institute of Science and Technology Austria, 2021.","mla":"Toman, Viktor. Improved Verification Techniques for Concurrent Systems. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10199.","apa":"Toman, V. (2021). Improved verification techniques for concurrent systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10199","ieee":"V. Toman, “Improved verification techniques for concurrent systems,” Institute of Science and Technology Austria, 2021.","ista":"Toman V. 2021. Improved verification techniques for concurrent systems. Institute of Science and Technology Austria.","ama":"Toman V. Improved verification techniques for concurrent systems. 2021. doi:10.15479/at:ista:10199"},"date_published":"2021-10-31T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The design and verification of concurrent systems remains an open challenge due to the non-determinism that arises from the inter-process communication. In particular, concurrent programs are notoriously difficult both to be written correctly and to be analyzed formally, as complex thread interaction has to be accounted for. The difficulties are further exacerbated when concurrent programs get executed on modern-day hardware, which contains various buffering and caching mechanisms for efficiency reasons. This causes further subtle non-determinism, which can often produce very unintuitive behavior of the concurrent programs. Model checking is at the forefront of tackling the verification problem, where the task is to decide, given as input a concurrent system and a desired property, whether the system satisfies the property. The inherent state-space explosion problem in model checking of concurrent systems causes naïve explicit methods not to scale, thus more inventive methods are required. One such method is stateless model checking (SMC), which explores in memory-efficient manner the program executions rather than the states of the program. State-of-the-art SMC is typically coupled with partial order reduction (POR) techniques, which argue that certain executions provably produce identical system behavior, thus limiting the amount of executions one needs to explore in order to cover all possible behaviors. Another method to tackle the state-space explosion is symbolic model checking, where the considered techniques operate on a succinct implicit representation of the input system rather than explicitly accessing the system. In this thesis we present new techniques for verification of concurrent systems. We present several novel POR methods for SMC of concurrent programs under various models of semantics, some of which account for write-buffering mechanisms. Additionally, we present novel algorithms for symbolic model checking of finite-state concurrent systems, where the desired property of the systems is to ensure a formally defined notion of fairness.","lang":"eng"}],"ddc":["000"],"status":"public","title":"Improved verification techniques for concurrent systems","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10199","oa_version":"Published Version","file":[{"file_id":"10225","relation":"main_file","checksum":"4f412a1ee60952221b499a4b1268df35","date_created":"2021-11-08T14:12:22Z","date_updated":"2021-11-08T14:12:22Z","access_level":"open_access","file_name":"toman_th_final.pdf","creator":"vtoman","content_type":"application/pdf","file_size":2915234},{"content_type":"application/zip","file_size":8616056,"creator":"vtoman","file_name":"toman_thesis.zip","access_level":"closed","date_updated":"2021-11-09T09:00:50Z","date_created":"2021-11-08T14:12:46Z","checksum":"9584943f99127be2dd2963f6784c37d4","relation":"source_file","file_id":"10226"}]},{"title":"On the adaptive security of graph-based games","ddc":["519"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10035","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"thesis_pdfa.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":2104726,"file_id":"10082","relation":"main_file","success":1,"checksum":"73a44345c683e81f3e765efbf86fdcc5","date_updated":"2021-10-04T12:22:33Z","date_created":"2021-10-04T12:22:33Z"},{"date_updated":"2022-03-10T12:15:18Z","date_created":"2021-10-05T07:04:37Z","checksum":"7b80df30a0e686c3ef6a56d4e1c59e29","file_id":"10085","relation":"source_file","creator":"cchlebak","file_size":9538359,"content_type":"application/x-zip-compressed","file_name":"thesis_final (1).zip","access_level":"closed"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for \"graph-building\" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c])."}],"page":"276","citation":{"chicago":"Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035.","short":"K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021.","mla":"Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035.","apa":"Klein, K. (2021). On the adaptive security of graph-based games. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035","ieee":"K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021.","ista":"Klein K. 2021. On the adaptive security of graph-based games. Institute of Science and Technology Austria.","ama":"Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035"},"date_published":"2021-09-23T00:00:00Z","day":"23","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"acknowledgement":"I want to acknowledge the funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).\r\n","year":"2021","date_created":"2021-09-23T07:31:44Z","date_updated":"2023-10-17T09:24:07Z","author":[{"last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"}],"related_material":{"record":[{"id":"10044","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10049"},{"id":"637","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10041"},{"id":"6430","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10048"}]},"file_date_updated":"2022-03-10T12:15:18Z","ec_funded":1,"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"supervisor":[{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10035","month":"09","publication_identifier":{"issn":["2663-337X"]}},{"date_published":"2021-12-09T00:00:00Z","page":"132","citation":{"mla":"Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429.","ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429","ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria.","apa":"Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021."},"has_accepted_license":"1","article_processing_charge":"No","day":"09","oa_version":"Published Version","file":[{"file_size":2370859,"content_type":"application/pdf","creator":"gnadirad","file_name":"Thesis_Final_09_12_2021.pdf","access_level":"open_access","date_updated":"2021-12-09T17:47:49Z","date_created":"2021-12-09T17:47:49Z","checksum":"6bf14e9a523387328f016c0689f5e10e","success":1,"relation":"main_file","file_id":"10436"},{"creator":"gnadirad","content_type":"application/zip","file_size":2596924,"file_name":"Thesis_Final_09_12_2021.zip","access_level":"closed","date_created":"2021-12-09T17:47:49Z","date_updated":"2022-03-28T12:55:12Z","checksum":"914d6c5ca86bd0add471971a8f4c4341","file_id":"10437","relation":"source_file"}],"ddc":["000"],"title":"On achieving scalability through relaxation","status":"public","_id":"10429","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently creates a race condition. This bottleneck can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the stochastic gradient descent (SGD) algorithm, which distribute computation among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"}],"doi":"10.15479/at:ista:10429","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"12","date_created":"2021-12-08T21:52:28Z","date_updated":"2023-10-17T11:48:55Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10432"},{"relation":"part_of_dissertation","status":"public","id":"6673"},{"relation":"part_of_dissertation","status":"public","id":"5965"},{"id":"10435","relation":"part_of_dissertation","status":"public"}]},"author":[{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"}],"department":[{"_id":"GradSch"},{"_id":"DaAl"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","ec_funded":1,"file_date_updated":"2022-03-28T12:55:12Z"},{"publication_identifier":{"issn":["2663-337X"]},"month":"08","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"},{"full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:9733","project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"ec_funded":1,"file_date_updated":"2022-03-10T12:13:57Z","date_updated":"2024-03-06T12:30:44Z","date_created":"2021-07-27T15:48:30Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9787"},{"relation":"part_of_dissertation","status":"public","id":"9792"},{"id":"9225","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9781"},{"status":"public","relation":"part_of_dissertation","id":"9791"}]},"author":[{"id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","first_name":"Dario","last_name":"Feliciangeli","full_name":"Feliciangeli, Dario"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"publication_status":"published","year":"2021","article_processing_charge":"No","has_accepted_license":"1","day":"20","date_published":"2021-08-20T00:00:00Z","page":"180","citation":{"mla":"Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733.","short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.","ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733","ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","apa":"Feliciangeli, D. (2021). The polaron at strong coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9733","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021."},"abstract":[{"lang":"eng","text":"This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"date_updated":"2021-09-06T09:28:56Z","date_created":"2021-08-19T14:03:48Z","checksum":"e88bb8ca43948abe060eb2d2fa719881","file_id":"9944","relation":"main_file","creator":"dfelicia","file_size":1958710,"content_type":"application/pdf","file_name":"Thesis_FeliciangeliA.pdf","access_level":"open_access"},{"file_id":"9945","relation":"source_file","date_updated":"2022-03-10T12:13:57Z","date_created":"2021-08-19T14:06:35Z","checksum":"72810843abee83705853505b3f8348aa","file_name":"thesis.7z","access_level":"closed","creator":"dfelicia","file_size":3771669,"content_type":"application/octet-stream"}],"ddc":["515","519","539"],"status":"public","title":"The polaron at strong coupling","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9733"},{"date_published":"2021-09-13T00:00:00Z","citation":{"ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","apa":"Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","mla":"Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992."},"page":"168","day":"13","article_processing_charge":"No","has_accepted_license":"1","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"9993","checksum":"c763064adaa720e16066c1a4f9682bbb","date_created":"2021-09-09T07:29:48Z","date_updated":"2021-09-15T22:30:26Z","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_vupload.docx","file_size":25179004,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"lhoermaye"},{"creator":"lhoermaye","content_type":"application/pdf","file_size":6246900,"access_level":"open_access","file_name":"Thesis_vfinal_pdfa.pdf","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","date_updated":"2021-09-15T22:30:26Z","date_created":"2021-09-09T14:25:08Z","file_id":"9996","embargo":"2021-09-09","relation":"main_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9992","ddc":["575"],"status":"public","title":"Wound healing in the Arabidopsis root meristem","abstract":[{"lang":"eng","text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:9992","supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"project":[{"name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"month":"09","publication_identifier":{"issn":["2663-337X"]},"author":[{"full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","first_name":"Lukas"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6351"},{"id":"6943","relation":"part_of_dissertation","status":"public"},{"id":"8002","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-09-07T13:38:33Z","date_created":"2021-09-09T07:37:20Z","year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"file_date_updated":"2021-09-15T22:30:26Z","ec_funded":1},{"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","date_updated":"2023-09-07T13:33:27Z","date_created":"2021-07-01T14:50:17Z","related_material":{"record":[{"id":"9750","status":"public","relation":"part_of_dissertation"},{"id":"9006","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","first_name":"Silvia"}],"file_date_updated":"2022-07-02T22:30:06Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"doi":"10.15479/at:ista:9623","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-012-1"]},"month":"07","status":"public","ddc":["570"],"title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9623","oa_version":"Published Version","file":[{"checksum":"e039225a47ef32666d59bf35ddd30ecf","date_created":"2021-07-01T14:48:54Z","date_updated":"2022-07-02T22:30:06Z","file_id":"9624","relation":"source_file","creator":"scaballe","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":131946790,"access_level":"closed","file_name":"PhDThesis_SCM.docx","embargo_to":"open_access"},{"relation":"main_file","embargo":"2022-07-01","file_id":"9625","date_updated":"2022-07-02T22:30:06Z","date_created":"2021-07-01T14:46:25Z","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","file_name":"PhDThesis_SCM.pdf","access_level":"open_access","file_size":17094958,"content_type":"application/pdf","creator":"scaballe"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n","lang":"eng"}],"page":"111","citation":{"chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","mla":"Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623.","apa":"Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623"},"date_published":"2021-07-01T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1"},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"doi":"10.15479/at:ista:10058","project":[{"call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["2663-337X"]},"month":"10","date_created":"2021-09-30T07:53:49Z","date_updated":"2023-09-08T11:41:08Z","related_material":{"record":[{"id":"8831","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10065"},{"id":"10066","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8909"},{"id":"5816","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publication_status":"published","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","year":"2021","file_date_updated":"2022-12-20T23:30:07Z","date_published":"2021-10-05T00:00:00Z","page":"151","citation":{"ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","apa":"Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058","ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058","chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058.","mla":"Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058.","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021."},"article_processing_charge":"No","has_accepted_license":"1","day":"05","keyword":["qubits","quantum computing","holes"],"oa_version":"Published Version","file":[{"relation":"source_file","file_id":"10061","date_updated":"2022-12-20T23:30:07Z","date_created":"2021-09-30T14:29:14Z","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","embargo_to":"open_access","file_name":"PHD_Thesis_Jirovec_Source.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":32397600,"creator":"djirovec"},{"date_created":"2021-10-05T07:56:49Z","date_updated":"2022-12-20T23:30:07Z","checksum":"5fbe08d4f66d1153e04c47971538fae8","relation":"main_file","file_id":"10087","embargo":"2022-10-06","file_size":26910829,"content_type":"application/pdf","creator":"djirovec","file_name":"PHD_Thesis_pdfa2b_1.pdf","access_level":"open_access"}],"status":"public","title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","ddc":["621","539"],"_id":"10058","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term. The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments."}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"status":"public","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","ddc":["571"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9397","oa_version":"Published Version","file":[{"access_level":"closed","embargo_to":"open_access","file_name":"KHuljev_Thesis_corrections.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":47799741,"creator":"khuljev","relation":"source_file","file_id":"9398","checksum":"7f98532f5324a0b2f3fa8de2967baa19","date_created":"2021-05-17T12:29:12Z","date_updated":"2022-05-21T22:30:04Z"},{"relation":"main_file","file_id":"9401","embargo":"2022-05-20","date_created":"2021-05-18T14:50:28Z","date_updated":"2022-05-21T22:30:04Z","checksum":"bf512f8a1e572a543778fc4b227c01ba","file_name":"new_KHuljev_Thesis_corrections.pdf","access_level":"open_access","file_size":16542131,"content_type":"application/pdf","creator":"khuljev"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation."}],"page":"101","citation":{"mla":"Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","apa":"Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021."},"date_published":"2021-05-18T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"18","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","date_created":"2021-05-17T12:31:30Z","date_updated":"2023-09-07T13:32:32Z","author":[{"full_name":"Huljev, Karla","first_name":"Karla","last_name":"Huljev","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2022-05-21T22:30:04Z","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:9397","publication_identifier":{"issn":["2663-337X"]},"month":"05"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry."}],"ddc":["570"],"title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9562","oa_version":"Published Version","file":[{"checksum":"659df5518db495f679cb1df9e9bd1d94","date_created":"2021-06-17T14:03:14Z","date_updated":"2022-07-02T22:30:04Z","file_id":"9563","embargo":"2022-07-01","relation":"main_file","creator":"dkleindienst","file_size":77299142,"content_type":"application/pdf","access_level":"open_access","file_name":"Thesis.pdf"},{"date_updated":"2022-07-02T22:30:04Z","date_created":"2021-06-17T14:04:30Z","checksum":"3bcf63a2b19e5b6663be051bea332748","relation":"source_file","file_id":"9564","file_size":369804895,"content_type":"application/zip","creator":"dkleindienst","embargo_to":"open_access","file_name":"Thesis_source.zip","access_level":"closed"}],"has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"124","citation":{"ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.","mla":"Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021."},"date_published":"2021-06-01T00:00:00Z","file_date_updated":"2022-07-02T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","date_updated":"2023-09-11T12:55:53Z","date_created":"2021-06-17T14:10:47Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9756"},{"id":"9437","relation":"part_of_dissertation","status":"public"},{"id":"8532","status":"public","relation":"part_of_dissertation"},{"id":"612","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Kleindienst, David","first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"month":"06","oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.15479/at:ista:9562"},{"status":"public","ddc":["005"],"title":"Parameterized and algebro-geometric advances in static program analysis","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8934","file":[{"embargo":"2021-12-22","file_id":"8969","relation":"main_file","date_created":"2020-12-22T20:08:44Z","date_updated":"2021-12-23T23:30:04Z","checksum":"d1b9db3725aed34dadd81274aeb9426c","file_name":"Thesis-pdfa.pdf","access_level":"open_access","creator":"akafshda","content_type":"application/pdf","file_size":5251507},{"file_id":"8970","relation":"source_file","date_updated":"2021-03-04T23:30:04Z","date_created":"2020-12-22T20:08:50Z","checksum":"1661df7b393e6866d2460eba3c905130","file_name":"source.zip","embargo_to":"open_access","access_level":"closed","creator":"akafshda","content_type":"application/zip","file_size":10636756}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades."}],"page":"278","citation":{"chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934.","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","mla":"Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934.","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","apa":"Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. 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Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","apa":"Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.","mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.","short":"K. 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Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response.","lang":"eng"}],"oa":1,"doi":"10.15479/at:ista:10307","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"supervisor":[{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Michael K","last_name":"Sixt"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"publication_identifier":{"issn":["2663-337X"]},"month":"11","year":"2021","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"10316","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","first_name":"Kathrin","last_name":"Tomasek"}],"date_created":"2021-11-18T15:05:06Z","date_updated":"2023-09-07T13:34:38Z","file_date_updated":"2022-12-20T23:30:05Z"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"supervisor":[{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:10303","publication_identifier":{"issn":["2663-337X"]},"month":"11","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","date_updated":"2023-09-19T14:42:45Z","date_created":"2021-11-18T11:20:59Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9010"},{"id":"9913","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"47"}]},"author":[{"last_name":"Abualia","first_name":"Rashed","orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed"}],"file_date_updated":"2022-12-20T23:30:06Z","page":"139","citation":{"ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","apa":"Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.","short":"R. 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Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. "}]}]